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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ), 'gf_id' => 'HOM05D001242', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001242' ), 'data_identifier' => 'HOM05D001242', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001242', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '502', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p07260' => 'bna', 'A02p07270' => 'bna', 'A03p11810' => 'bna', 'A03p11820' => 'bna', 'A05p08060' => 'bna', 'A06p20650' => 'bna', 'A10p16440' => 'bna', 'A10p16470' => 'bna', 'Aa31LG1G11730' => 'aar', 'Aa31LG1G11740' => 'aar', 'Aa31LG4G15850' => 'aar', 'Aa31sc250G60' => 'aar', 'Actinidia23910' => 'ach', 'Actinidia29157' => 'ach', 'Ah.02g119520' => 'amhyb', 'Ah.08g220340' => 'amhyb', 'Ah.15g100190' => 'amhyb', 'AL4G20270' => 'aly', 'AL4G34870' => 'aly', 'AL5G25930' => 'aly', 'AL7G44450' => 'aly', 'AL8G35670' => 'aly', 'AL8G35680' => 'aly', 'Aqoxy1G00782' => 'aox', 'Aqoxy1G00783' => 'aox', 'Aqoxy1G00784' => 'aox', 'Aqoxy1G03955' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2DI66Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4UA1TJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8PB3CL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HBBD6V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IUYA4Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QJ2G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSS812' => 'arhy', 'AT2G26975' => 'ath', 'AT2G37925' => 'ath', 'AT3G46900' => 'ath', 'AT5G59030' => 'ath', 'AT5G59040' => 'ath', 'ATR0210G026' => 'atr', 'ATR0210G045' => 'atr', 'Atru.chr1.529' => 'acertr', 'Atru.chr3.4034' => 'acertr', 'Atru.chr3.4035' => 'acertr', 'Atru.chr3.4036' => 'acertr', 'Atru.chr3.4037' => 'acertr', 'Atru.chr8.2108' => 'acertr', 'Atru.chr8.2109' => 'acertr', 'AUR62001720' => 'cqu', 'AUR62020059' => 'cqu', 'AUR62020063' => 'cqu', 'AUR62020064' => 'cqu', 'AUR62029441' => 'cqu', 'BcaB01g00962' => 'bca', 'BcaB01g04599' => 'bca', 'BcaB01g04600' => 'bca', 'BcaB02g09236' => 'bca', 'BcaB05g22501' => 'bca', 'BcaB05g22503' => 'bca', 'BcaB08g36272' => 'bca', 'BcaB08g36273' => 'bca', 'BcaB08g36274' => 'bca', 'BcaC01g01869' => 'bca', 'BcaC02g11920' => 'bca', 'BcaC02g11921' => 'bca', 'BcaC03g14027' => 'bca', 'BcaC03g14028' => 'bca', 'BcaC03g14029' => 'bca', 'BcaC04g19801' => 'bca', 'BcaC04g19803' => 'bca', 'BcaC09g49783' => 'bca', 'BolC1t03237H' => 'bol', 'BolC2t07365H' => 'bol', 'BolC2t07366H' => 'bol', 'BolC2t07367H' => 'bol', 'BolC3t13834H' => 'bol', 'BolC3t13835H' => 'bol', 'BolC3t19391H' => 'bol', 'BolC4t22601H' => 'bol', 'BolC9t58008H' => 'bol', 'BolC9t58012H' => 'bol', 'BraA02t05805Z' => 'bra', 'BraA02t05806Z' => 'bra', 'BraA03t10492Z' => 'bra', 'BraA03t10493Z' => 'bra', 'BraA05t19774Z' => 'bra', 'BraA06t25144Z' => 'bra', 'BraA10t43728Z' => 'bra', 'BraA10t43730Z' => 'bra', 'C01p32980' => 'bna', 'C02p12670' => 'bna', 'C02p12680' => 'bna', 'C02p12690' => 'bna', 'C03p13870' => 'bna', 'C03p13880' => 'bna', 'C03p71080' => 'bna', 'C04p09960' => 'bna', 'C09p51490' => 'bna', 'C09p51530' => 'bna', 'C09p51550' => 'bna', 'CAN.G1101.5' => 'can', 'CAN.G1267.2' => 'can', 'CAN.G1307.4' => 'can', 'CAN.G137.55' => 'can', 'CAN.G502.12' => 'can', 'CANSAT35G0277' => 'cansat', 'CANSAT35G0635' => 'cansat', 'CANSAT35G0959' => 'cansat', 'CANSAT54G2976' => 'cansat', 'CANSAT56G1941' => 'cansat', 'CARHR132470' => 'chi', 'CARHR155490' => 'chi', 'CARHR285580' => 'chi', 'CARHR285590' => 'chi', 'Carub.0004s1983' => 'cru', 'Carub.0005s1312' => 'cru', 'Carub.0008s1990' => 'cru', 'Carub.0008s1991' => 'cru', 'Ca_03544_v3' => 'car', 'Ca_07583_v3' => 'car', 'Ca_07584_v3' => 'car', 'Ca_20571_v3' => 'car', 'Ca_20606_v3' => 'car', 'Ca_30506_v3' => 'car', 'Cc01_g13550' => 'ccan', 'Cc01_g13560' => 'ccan', 'Cc06_g01980' => 'ccan', 'Cc06_g02000' => 'ccan', 'CDE02G3205' => 'cde', 'CDE04G1106' => 'cde', 'Cfa011591' => 'cfa', 'Cfa011592' => 'cfa', 'Cfa017292' => 'cfa', 'Ciclev10013024m.g' => 'ccl', 'Ciclev10013520m.g' => 'ccl', 'Ciclev10027063m.g' => 'ccl', 'Ciclev10029475m.g' => 'ccl', 'Ciclev10029496m.g' => 'ccl', 'Ciclev10029506m.g' => 'ccl', 'Ciclev10029806m.g' => 'ccl', 'Ciclev10029961m.g' => 'ccl', 'Ciclev10030036m.g' => 'ccl', 'Ciclev10033440m.g' => 'ccl', 'CiPaw.09G202900' => 'cil', 'CiPaw.09G203000' => 'cil', 'CiPaw.09G203100' => 'cil', 'CiPaw.10G150400' => 'cil', 'CiPaw.10G150700' => 'cil', 'CiPaw.13G086800' => 'cil', 'CiPaw.14G063400' => 'cil', 'CiPaw.14G063500' => 'cil', 'ClCG00G003070' => 'cla', 'ClCG03G001130' => 'cla', 'ClCG03G001140' => 'cla', 'ClCG04G007530' => 'cla', 'ClCG10G021610' => 'cla', 'COL.COLO4_14483' => 'col', 'COL.COLO4_14674' => 'col', 'COL.COLO4_14679' => 'col', 'COL.COLO4_19054' => 'col', 'COL.COLO4_19055' => 'col', 'COL.COLO4_19056' => 'col', 'Cpa.g.sc56.72' => 'cpa', 'Cpa.g.sc56.73' => 'cpa', 'Cpa.g.sc81.49' => 'cpa', 'CsaV3_1G034650' => 'csa', 'CsaV3_1G035760' => 'csa', 'CsaV3_1G035770' => 'csa', 'CsaV3_3G034410' => 'csa', 'CsaV3_4G025720' => 'csa', 'CSS0001360' => 'camsi', 'CSS0015656' => 'camsi', 'CSS0022530' => 'camsi', 'CSS0038529' => 'camsi', 'CSS0045778' => 'camsi', 'CSS0050451' => 'camsi', 'DCAR_007413' => 'dca', 'DCAR_007414' => 'dca', 'DCAR_010431' => 'dca', 'DCAR_010432' => 'dca', 'DCAR_012150' => 'dca', 'Dinv17069' => 'din', 'Dinv34307' => 'din', 'Dinv37106' => 'din', 'Dinv43013' => 'din', 'Dinv43084' => 'din', 'Duzib093G0012' => 'dzi', 'Duzib093G1541' => 'dzi', 'Duzib128G0201' => 'dzi', 'Duzib150G0599' => 'dzi', 'Duzib168G0656' => 'dzi', 'Duzib170G0043' => 'dzi', 'Duzib170G0338' => 'dzi', 'ECA236G4199' => 'eca', 'ECA248G0340' => 'eca', 'ECA248G2536' => 'eca', 'EL10Ac7g16092' => 'bvu', 'Eucgr.B02736' => 'egr', 'Eucgr.B02737' => 'egr', 'Eucgr.B02742' => 'egr', 'Eucgr.J01974' => 'egr', 'Eucgr.J01987' => 'egr', 'Eucgr.J01988' => 'egr', 'Eucgr.J01990' => 'egr', 'Eucgr.J01991' => 'egr', 'Eucgr.J01992' => 'egr', 'Eucgr.J01994' => 'egr', 'Eucgr.K03017' => 'egr', 'FAN05G1299' => 'fan', 'FAN05G4545' => 'fan', 'FAN09G1799' => 'fan', 'FAN11G2853' => 'fan', 'FAN14G3341' => 'fan', 'FAN16G0096' => 'fan', 'FAN25G1433' => 'fan', 'FvH4_3g37240' => 'fve', 'FvH4_6g12620' => 'fve', 'FvH4_6g12630' => 'fve', 'Glyma.01G106700' => 'gma', 'Glyma.07G141200' => 'gma', 'Glyma.07G141600' => 'gma', 'Glyma.11G134700' => 'gma', 'Glyma.18G191300' => 'gma', 'Glyma.18G191900' => 'gma', 'Gohir.A01G223800' => 'ghi', 'Gohir.A03G046150' => 'ghi', 'Gohir.A03G046800' => 'ghi', 'Gohir.A03G046900' => 'ghi', 'Gohir.A05G091800' => 'ghi', 'Gohir.A08G001700' => 'ghi', 'Gohir.A13G086100' => 'ghi', 'Gohir.D01G212900' => 'ghi', 'Gohir.D03G120300' => 'ghi', 'Gohir.D03G120400' => 'ghi', 'Gohir.D03G121000' => 'ghi', 'Gohir.D05G092650' => 'ghi', 'Gohir.D08G012400' => 'ghi', 'Gohir.D13G099000' => 'ghi', 'Gorai.002G148700' => 'gra', 'Gorai.002G259000' => 'gra', 'Gorai.003G126900' => 'gra', 'Gorai.003G127000' => 'gra', 'Gorai.003G128000' => 'gra', 'Gorai.004G006400' => 'gra', 'Gorai.009G095200' => 'gra', 'GSVIVG01012309001' => 'vvi', 'GSVIVG01012313001' => 'vvi', 'GSVIVG01024838001' => 'vvi', 'GSVIVG01024839001' => 'vvi', 'GSVIVG01024841001' => 'vvi', 'HanXRQChr00c0423g0574651' => 'han', 'HanXRQChr04g0124611' => 'han', 'HanXRQChr05g0149911' => 'han', 'HanXRQChr08g0234561' => 'han', 'HanXRQChr08g0237541' => 'han', 'HanXRQChr11g0339181' => 'han', 'HanXRQChr17g0552641' => 'han', 'HanXRQChr17g0568201' => 'han', 'Haze_20901' => 'cav', 'Haze_24209' => 'cav', 'Haze_24210' => 'cav', 'Haze_24211' => 'cav', 'Hma1.2p1_0274F.1_g110390' => 'hma', 'Hma1.2p1_1521F.1_g288680' => 'hma', 'Hma1.2p1_1521F.1_g288690' => 'hma', 'HPP92_001775' => 'vpl', 'HPP92_018163' => 'vpl', 'HPP92_018176' => 'vpl', 'HPP92_019860' => 'vpl', 'Lalb_Chr01g0003431' => 'lal', 'Lalb_Chr19g0124941' => 'lal', 'Lalb_Chr19g0138051' => 'lal', 'Lalb_Chr19g0138061' => 'lal', 'Lj1g0006381' => 'lja', 'Lj1g0025264' => 'lja', 'Lj2C85T2' => 'lonja', 'Lj2C85T5' => 'lonja', 'Lj2P1071T11' => 'lonja', 'Lj3A421G11' => 'lonja', 'Lj3C420T1' => 'lonja', 'Lj3g0014463' => 'lja', 'Lj3P959T36' => 'lonja', 'LjContig00047_ERROPOS266959g0007637' => 'lja', 'Lsat_1_v5_gn_5_168280' => 'lsa', 'Lsat_1_v5_gn_5_168340' => 'lsa', 'Lsat_1_v5_gn_8_80780' => 'lsa', 'Lsat_1_v5_gn_9_24241' => 'lsa', 'Lsat_1_v5_gn_9_31101' => 'lsa', 'Manes.01G167200' => 'mes', 'Manes.02G125400' => 'mes', 'Manes.02G125500' => 'mes', 'Manes.08G082600' => 'mes', 'Manes.09G099200' => 'mes', 'Mapoly0013s0019' => 'mpo', 'MBI05_g02675_MAGBIO' => 'mbi', 'MBI14_g02852_MAGBIO' => 'mbi', 'MD03G1082600' => 'mdo', 'MD04G1140400' => 'mdo', 'MD04G1140500' => 'mdo', 'MD07G1250000' => 'mdo', 'MD10G1019100' => 'mdo', 'MD11G1090600' => 'mdo', 'MD12G1155800' => 'mdo', 'MD12G1155900' => 'mdo', 'MD12G1156000' => 'mdo', 'Medtr0027s0220' => 'mtr', 'Medtr4g019870' => 'mtr', 'Medtr4g064963' => 'mtr', 'Medtr4g065123' => 'mtr', 'Medtr4g065660' => 'mtr', 'Medtr7g066070' => 'mtr', 'MELO3C003197.2' => 'cme', 'MELO3C009211.2' => 'cme', 'MELO3C020592.2' => 'cme', 'MELO3C020593.2' => 'cme', 'MELO3C020594.2' => 'cme', 'Migut.J00257' => 'egut', 'Migut.J00982' => 'egut', 'Migut.L01978' => 'egut', 'Migut.N00818' => 'egut', 'Migut.N00911' => 'egut', 'Migut.N02571' => 'egut', 'MSTRG.12658' => 'ama', 'MSTRG.12659' => 'ama', 'MSTRG.17823' => 'ama', 'MSTRG.26789' => 'ama', 'MSTRG.5619' => 'ama', 'Nitab4.5_0000008g0250' => 'nta', 'Nitab4.5_0000102g0450' => 'nta', 'Nitab4.5_0000131g0260' => 'nta', 'Nitab4.5_0000652g0070' => 'nta', 'Nitab4.5_0000880g0110' => 'nta', 'Nitab4.5_0000994g0050' => 'nta', 'Nitab4.5_0002823g0050' => 'nta', 'Nitab4.5_0002823g0090' => 'nta', 'Nitab4.5_0003264g0020' => 'nta', 'Nitab4.5_0003709g0020' => 'nta', 'Nitab4.5_0009383g0010' => 'nta', 'Nn2g11299' => 'nnu', 'Nn2g11301' => 'nnu', 'Nn2g13537' => 'nnu', 'Nn2g14682' => 'nnu', 'Nn7g36923' => 'nnu', 'Oeu001827.1' => 'oeu', 'Oeu001828.1' => 'oeu', 'Oeu014999.1' => 'oeu', 'Oeu022265.1' => 'oeu', 'Oeu030420.1' => 'oeu', 'Oeu045619.1' => 'oeu', 'Oeu053877.1' => 'oeu', 'Os01g0770700' => 'osa', 'Os01g0770800' => 'osa', 'Os03g0370800' => 'osa', 'Os04g0415600' => 'osa', 'Os05g0424700' => 'osa', 'Peaxi162Scf00009g10337' => 'pax', 'Peaxi162Scf00179g00097' => 'pax', 'Peaxi162Scf00664g00032' => 'pax', 'Peaxi162Scf00765g00012' => 'pax', 'PGR031G0435' => 'pgr', 'PGR031G0974' => 'pgr', 'PGR119G0451' => 'pgr', 'PGR119G0465' => 'pgr', 'PGR119G1867' => 'pgr', 'PGSC0003DMG400009540' => 'stu', 'PGSC0003DMG400011086' => 'stu', 'PGSC0003DMG400011720' => 'stu', 'PGSC0003DMG400020829' => 'stu', 'PGSC0003DMG400023142' => 'stu', 'PGSC0003DMG400042351' => 'stu', 'Phvul.008G112800' => 'pvu', 'Phvul.008G113200' => 'pvu', 'Phvul.011G060400' => 'pvu', 'Phvul.011G060500' => 'pvu', 'Potri.001G246000' => 'ptr', 'Potri.006G093200' => 'ptr', 'Potri.006G093300' => 'ptr', 'Potri.009G038700' => 'ptr', 'Potri.009G038800' => 'ptr', 'Prupe.6G007600' => 'ppe', 'Prupe.6G066900' => 'ppe', 'Prupe.6G265500' => 'ppe', 'Prupe.6G265600' => 'ppe', 'Prupe.6G265700' => 'ppe', 'Prupe.6G266000' => 'ppe', 'Psat3g134920' => 'psa', 'Psat3g134960' => 'psa', 'Psat7g211560' => 'psa', 'Psat7g213120' => 'psa', 'Psat7g241040' => 'psa', 'PSO339G5955' => 'pso', 'PSO339G6310' => 'pso', 'PSO384G0820' => 'pso', 'PSO384G4070' => 'pso', 'PSO675G6066' => 'pso', 'PSO732G0677' => 'pso', 'QL01p028360' => 'qlo', 'QL01p028381' => 'qlo', 'QL01p028394' => 'qlo', 'QL01p028397' => 'qlo', 'QL07p027886' => 'qlo', 'QL07p027913' => 'qlo', 'RcHm_v2.0_Chr3g0464451' => 'rch', 'RcHm_v2.0_Chr3g0464471' => 'rch', 'RcHm_v2.0_Chr3g0464481' => 'rch', 'RcHm_v2.0_Chr5g0066991' => 'rch', 'RcHm_v2.0_Chr5g0067001' => 'rch', 'Rhsim01G0233500' => 'rsi', 'Rhsim01G0233600' => 'rsi', 'Rhsim04G0163400' => 'rsi', 'Rhsim04G0163700' => 'rsi', 'Rhsim13G0075800' => 'rsi', 'Sabra06G0070900' => 'sbr', 'Sabra06G0071000' => 'sbr', 'Sabra09G0027600' => 'sbr', 'Sabra09G0027700' => 'sbr', 'SalBow1G6921' => 'sbo', 'SalBow2G1596' => 'sbo', 'SalBow2G3158' => 'sbo', 'SalBow2G3405' => 'sbo', 'SalBow4G2084' => 'sbo', 'Sc01g0004910' => 'sci', 'Sc12g0001140' => 'sci', 'Sc12g0001150' => 'sci', 'Sed0011823' => 'sed', 'Sed0012044' => 'sed', 'Sed0013304' => 'sed', 'Sed0023519' => 'sed', 'Sed0023574' => 'sed', 'Sed0025762' => 'sed', 'SEGI_28376' => 'sgi', 'SGA_v2.0_scaffold55G19704' => 'sas', 'SGA_v2.0_scaffold85G26807' => 'sas', 'SGA_v2.0_scaffold94G28556' => 'sas', 'SMO001G0023' => 'smo', 'SMO307G0071' => 'smo', 'Solyc06g005820.3' => 'sly', 'Solyc06g005825.1' => 'sly', 'Solyc08g006250.2' => 'sly', 'Solyc09g011665.1' => 'sly', 'Solyc09g011700.1' => 'sly', 'Solyc09g014870.1' => 'sly', 'Solyc10g084980.3' => 'sly', 'Sopen06g001800' => 'spe', 'Sopen08g002230' => 'spe', 'Sopen09g006480' => 'spe', 'Sopen09g007790' => 'spe', 'Sopen10g034440' => 'spe', 'Sp4g20230' => 'spa', 'Sp5g14840' => 'spa', 'Sp5g14850' => 'spa', 'Sp6g20930' => 'spa', 'Sp6g20940' => 'spa', 'TAR369G0371' => 'tar', 'TAR623G0757' => 'tar', 'TAR623G1015' => 'tar', 'TAR623G1624' => 'tar', 'TAR633G0979' => 'tar', 'TAR633G1783' => 'tar', 'THA.LOC104799417' => 'tha', 'THA.LOC104799418' => 'tha', 'THA.LOC104806537' => 'tha', 'THA.LOC104810741' => 'tha', 'THA.LOC104810742' => 'tha', 'Thecc.05G027400' => 'tca', 'Thecc.05G027600' => 'tca', 'Thecc.09G311300' => 'tca', 'Thecc.09G311400' => 'tca', 'Thecc.09G311500' => 'tca', 'Thhalv10010785m.g' => 'esa', 'Thhalv10014878m.g' => 'esa', 'Thhalv10015395m.g' => 'esa', 'Thhalv10017371m.g' => 'esa', 'TPR.G13634' => 'tpr', 'TPR.G13645' => 'tpr', 'TPR.G17897' => 'tpr', 'TPR.G23593' => 'tpr', 'TPR.G23637' => 'tpr', 'TPR.G30543' => 'tpr', 'TPR.G33181' => 'tpr', 'TPR.G35028' => 'tpr', 'TPR.G35034' => 'tpr', 'TWI31G0080' => 'twi', 'TWI31G0658' => 'twi', 'TWI31G0846' => 'twi', 'TWI31G1105' => 'twi', 'TWI31G1227' => 'twi', 'TWI53G0663' => 'twi', 'TWI53G1754' => 'twi', 'TWI77G0536' => 'twi', 'TWI79G0843' => 'twi', 'TWI79G1786' => 'twi', 'unitig_37.g12244' => 'ugi', 'unitig_578.g15886' => 'ugi', 'unitig_8.g4428' => 'ugi', 'vmacro03016' => 'vma', 'VMungo1127G1090' => 'vmu', 'VMungo1383G3516' => 'vmu', 'VMungo1383G3653' => 'vmu', 'Zm00001eb083630' => 'zma', 'Zm00001eb151980' => 'zma', 'Zm00001eb201000' => 'zma' ) $gf_id = 'HOM05D001242' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001242' ) $data_identifier = 'HOM05D001242' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 4, 'ach' => (int) 2, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 7, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 5, 'cansat' => (int) 5, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 10, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 6, 'cpa' => (int) 3, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 11, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 9, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 5, 'stu' => (int) 6, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 9, 'twi' => (int) 10, 'ugi' => (int) 3, 'vma' => (int) 1, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb201000' $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